J’ai trouvé ces figures qui permettraient de présenter plus que juste la médiane par molécule…
#Open the datasets
max <- read.csv("data/max.csv")
min <- read.csv("data/min.csv")
mol.med <- read.csv("data/mol.csv")
min$Year <- factor(min$Year)
max$Year <- factor(max$Year)
max$Route <- factor(max$Route)
mol.med$Year <- factor(mol.med$Year)
#Rename Route
max$Route <- ifelse(max$Route=="IM_L", "IMM-Lactation",
ifelse(max$Route=="IM_T", "IMM-Tarissement",
ifelse(max$Route=="INJ", "Injectable",
ifelse(max$Route=="IU", "IU",
ifelse(max$Route=="ORAL", "PO", "Topique")))))#Categorie 1
library(plotly)## Le chargement a nécessité le package : ggplot2##
## Attachement du package : 'plotly'## L'objet suivant est masqué depuis 'package:ggplot2':
##
## last_plot## L'objet suivant est masqué depuis 'package:stats':
##
## filter## L'objet suivant est masqué depuis 'package:graphics':
##
## layoutfig <- plot_ly(min,
x = ~Year,
y = ~POLYMYXINB_SULF_DCD,
type = 'box',
name="Polymixine B",
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~CEFTIOFUR_DCD,
type = 'box',
name="Ceftiofur",
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~DANOFLOXACIN_DCD,
type = 'box',
name="Danofloxacin",
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~ENROFLOXACIN_DCD,
type = 'box',
name="Enrofloxacin",
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~MARBOFLOXACIN_DCD,
type = 'box',
name="Marbofloxacin",
marker=list(color="white")
)
fig.cat1.mol <- fig %>%
layout(boxmode="group",
title = 'Utilisation des antibiotiques de catégorie I par molécule',
yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
hoverformat = '.0f',
range = list(0, 90)) #Adjust the y axis range
)
fig.cat1.mol## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'#Categorie 2
fig <- plot_ly(min,
x = ~Year,
y = ~GAMITROMYCIN_DCD,
type = 'box',
name="Gamitromycine",
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~TILDIPIROSIN_DCD,
name = 'Tildipirosine',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~TILMICOSIN_DCD,
name = 'Tilmicosine',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~TULATHROMYCIN_DCD,
name = 'Tulathromycine',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~TYLOSIN_DCD,
name = 'Tylosine',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~AMPICILLIN_DCD,
name="Ampicilline",
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~NEOMYCIN_SULF_DCD,
name = 'Neomycine',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~STREPTOMYCIN_SULF_DCD,
name = 'Streptomycine',
type = 'box',
marker=list(color="white")
)
fig.cat2b.mol <- fig %>%
layout(boxmode="group",
title = 'Utilisation des antibiotiques de catégorie II par molécule (partie 2/2)',
yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
hoverformat = '.0f',
range = list(0, 4)) #Adjust the y axis range
)
fig.cat2b.mol## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'#Categorie 2
fig <- plot_ly(min,
x = ~Year,
y = ~DIHYDROSTREPTOMYCIN_DCD,
name = 'Dihydrostreptomycine',
type="box",
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~CEFAPIRIN_DCD,
name = 'Céphapirine',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~PIRLIMYCIN_DCD,
name = 'Pirlimycine',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~CLOXACILLIN_DCD,
name = 'Cloxacilline',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~BENZYLPENICILLIN_B_DCD,
name = 'Benzylpenicilline B',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~BENZYLPENICILLIN_P_DCD,
name = 'Benzylpenicilline P',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~TRIM_SULFADOXINE_DCD,
name = 'Trimethoprim-sulfa',
type = 'box',
marker=list(color="white")
)
fig.cat2a.mol <- fig %>%
layout(boxmode="group",
title = 'Utilisation des antibiotiques de catégorie II par molécule (partie 1/2)',
yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
hoverformat = '.0f',
range = list(0, 160)) #Adjust the y axis range
)
fig.cat2a.mol## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'#Categorie 3
fig <- plot_ly(min,
x = ~Year,
y = ~CHLORTETRACYCLINE_DCD,
type = 'box',
name="Chlortetracycline",
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~OXYTETRACYCLINE_DCD,
name = 'Oxytetracycline',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~TETRACYCLINE_DCD,
name = 'Tetracycline',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~SUCCINYLSULFATHIAZOLE_DCD,
name = 'Succinyl Sulfathiazole',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~SULFAGUANIDINE_DCD,
name = 'Sulfaguanidine',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~SULFAMERAZINE_DCD,
name = 'Sulfamerazine',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~SULFAMETHAZINE_DCD,
name = 'Sulfamethazine',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~SULFANILAMIDE_DCD,
name = 'Sulfanilamide',
type = 'box',
marker=list(color="white")
)
fig <- fig %>% add_trace(min,
x = ~Year,
y = ~SULFATHIAZOLE_DCD,
name = 'Sulfathiazole',
type = 'box',
marker=list(color="white")
)
fig.cat3.mol <- fig %>%
layout(boxmode="group",
title = 'Utilisation des antibiotiques de catégorie III par molécule',
yaxis = list(title = "Taux d'utilisation (Traitement/100 animaux-année)",
hoverformat = '.0f',
range = list(0, 20)) #Adjust the y axis range
)
fig.cat3.mol## Warning: 'layout' objects don't have these attributes: 'boxmode'
## Valid attributes include:
## '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'